Abstract Background Atypical teratoid rhabdoid tumors (ATRT) are aggressive childhood central nervous system tumors that most often affect infants and children under age 3. Recent DNA methylation and transcriptomic profiling identified three molecular subgroups of ATRT – ATRT-TYR, ATRT-MYC, and ATRT-SHH. However, current multimodal therapy fails to distinguish between molecular subgroups, thus highlighting the need for ATRT subgroup-specific treatment strategies. Methods We harnessed subgroup-specific analyses of genome-scale CRISPR-Cas9 loss of function depletion screens in patient-derived ATRT cells to identify dependencies specific to the ATRT-MYC and ATRT-SHH subgroups. Candidate vulnerabilities underwent validation utilizing functional genomics approaches, including CRISPR-Cas9 knockout, Western blotting, cell viability assays, time lapse imaging of neurosphere formation, pharmacologic assays, and metabolic profiling. Results Analysis of genome-scale CRISPR-Cas9 loss of function screens in patient-derived ATRT cells identified significant genetic dependencies based on guide RNA (sgRNA) depletion. We then performed subgroup-specific analyses to extract those dependencies exclusive to either ATRT-MYC or ATRT-SHH cells. Using this unbiased approach, ATRT-MYC-specific dependencies appeared to be involved in mitochondrial complex I of the electron transport chain. Two genes emerged as ATRT-SHH-specific vulnerabilities, both converging on the squalene biosynthesis pathway, a critical precursor for cholesterol synthesis. We subsequently utilized low throughput CRISPR-Cas9 genetic knockout of each candidate gene in patient-derived ATRT-MYC (BT-16) and ATRT-SHH (CHLA-05-ATRT) cells to confirm the subtype-specific dependencies, assaying both cell viability and neurosphere formation. Western blot confirmed loss of protein expression of each candidate. Importantly, these pathways can be targeted by pharmacologic inhibition. Conclusion Here we define ATRT subgroup-specific vulnerabilities, demonstrating a rational approach to ATRT subgroup-specific therapy. This work provides high translational potential and the possibility of disease-altering benefits to patients affected by ATRT.
Larsen et al. (Tue,) studied this question.